void QmitkDeformableRegistrationView::ApplyDeformationField()
{

  ImageReaderType::Pointer reader  = ImageReaderType::New();
  reader->SetFileName( m_Controls.m_QmitkBSplineRegistrationViewControls->m_Controls.m_DeformationField->text().toStdString() );
  reader->Update();

  DeformationFieldType::Pointer deformationField = reader->GetOutput();

  mitk::Image * mimage = dynamic_cast<mitk::Image*> (m_MovingNode->GetData());
  mitk::Image * fimage = dynamic_cast<mitk::Image*> (m_FixedNode->GetData());

  typedef itk::Image<float, 3> FloatImageType;

  FloatImageType::Pointer itkMovingImage = FloatImageType::New();
  FloatImageType::Pointer itkFixedImage = FloatImageType::New();
  mitk::CastToItkImage(mimage, itkMovingImage);
  mitk::CastToItkImage(fimage, itkFixedImage);

  typedef itk::WarpImageFilter<
                            FloatImageType,
                            FloatImageType,
                            DeformationFieldType  >     WarperType;

  typedef itk::LinearInterpolateImageFunction<
                                    FloatImageType,
                                    double          >  InterpolatorType;

  WarperType::Pointer warper = WarperType::New();
  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  warper->SetInput( itkMovingImage );
  warper->SetInterpolator( interpolator );
  warper->SetOutputSpacing( itkFixedImage->GetSpacing() );
  warper->SetOutputOrigin( itkFixedImage->GetOrigin() );
  warper->SetOutputDirection (itkFixedImage->GetDirection() );
  warper->SetDisplacementField( deformationField );
  warper->Update();

  FloatImageType::Pointer outputImage = warper->GetOutput();
  mitk::Image::Pointer result = mitk::Image::New();

  mitk::CastToMitkImage(outputImage, result);

  // Create new DataNode
  mitk::DataNode::Pointer newNode = mitk::DataNode::New();
  newNode->SetData( result );
  newNode->SetProperty( "name", mitk::StringProperty::New("warped image") );

  // add the new datatree node to the datatree
  this->GetDefaultDataStorage()->Add(newNode);
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();

  //Image::Pointer outputImage = this->GetOutput();
  //mitk::CastToMitkImage( warper->GetOutput(), outputImage );


}
Exemplo n.º 2
0
  void TractAnalyzer::MakeRoi()
  {

    m_CostSum = 0.0;

    int n = 0;
    if(m_PointSetNode.IsNotNull())
    {
      n = m_PointSetNode->GetSize();
      if(n==0)
      {
        QMessageBox msgBox;
        msgBox.setText("No points have been set yet.");
        msgBox.exec();
      }
    }
    else{
      QMessageBox msgBox;
      msgBox.setText("No points have been set yet.");
      msgBox.exec();
    }

    std::string pathDescription = "";
    std::vector< itk::Index<3> > totalPath;

    if(n>0)
    {
      for(int i=0; i<n-1; ++i)
      {

        mitk::ProgressBar::GetInstance()->Progress();

        mitk::Point3D p = m_PointSetNode->GetPoint(i);
        mitk::Point3D p2 = m_PointSetNode->GetPoint(i+1);


        itk::Index<3> startPoint;
        itk::Index<3> endPoint;

        m_InputImage->GetGeometry()->WorldToIndex(p,startPoint);
        m_InputImage->GetGeometry()->WorldToIndex(p2,endPoint);

        MITK_INFO << "create roi";

        std::vector< itk::Index<3> > path = CreateSegment(startPoint, endPoint);

        for(std::vector< itk::Index<3> >::iterator it = path.begin();
            it != path.end(); it++)
        {
          itk::Index<3> ix = *it;

          if (!(ix==endPoint))
          {
            mitk::ProgressBar::GetInstance()->Progress();

            totalPath.push_back(ix);
            std::stringstream ss;
            ss << ix[0] << " " << ix[1] << " " << ix[2] << "\n";
            pathDescription += ss.str();
          }
          else
          {
            // Only when dealing with the last segment the last point should be added. This one will not occur
            // as the first point of the next roi segment.
            if(i == (n-2))
            {
              totalPath.push_back(endPoint);
              std::stringstream ss;
              ss << endPoint[0] << " " << endPoint[1] << " " << endPoint[2] << "\n";
              pathDescription += ss.str();
            }

          }

        }

      }


      // save pathDescription to m_PathDescription
      m_PathDescription = pathDescription;

      FloatImageType::Pointer itkImg = FloatImageType::New();
      mitk::CastToItkImage(m_InputImage, itkImg);

      CharImageType::Pointer roiImg = CharImageType::New();
      roiImg->SetRegions(itkImg->GetLargestPossibleRegion().GetSize());
      roiImg->SetOrigin(itkImg->GetOrigin());
      roiImg->SetSpacing(itkImg->GetSpacing());
      roiImg->SetDirection(itkImg->GetDirection());
      roiImg->Allocate();
      roiImg->FillBuffer(0);


      std::vector< itk::Index<3> > roi;

      std::vector< itk::Index<3> >::iterator it;
      for(it = totalPath.begin();
          it != totalPath.end();
          it++)
      {
        itk::Index<3> ix = *it;
        roiImg->SetPixel(ix, 1);
        roi.push_back(ix);
      }


      m_TbssRoi = mitk::TbssRoiImage::New();

      m_TbssRoi->SetRoi(roi);

      m_TbssRoi->SetImage(roiImg);

      m_TbssRoi->InitializeFromImage();



    }



  }
Exemplo n.º 3
0
static void
ExtractSlicesFromImages(mitk::Image::Pointer image, mitk::Image::Pointer mask,
                        mitk::Image::Pointer maskNoNaN, mitk::Image::Pointer morphMask,
                        int direction,
                        std::vector<mitk::Image::Pointer> &imageVector,
                        std::vector<mitk::Image::Pointer> &maskVector,
                        std::vector<mitk::Image::Pointer> &maskNoNaNVector,
                        std::vector<mitk::Image::Pointer> &morphMaskVector)
{
  typedef itk::Image< double, 2 >                 FloatImage2DType;
  typedef itk::Image< unsigned short, 2 >          MaskImage2DType;

  FloatImageType::Pointer itkFloat = FloatImageType::New();
  MaskImageType::Pointer itkMask = MaskImageType::New();
  MaskImageType::Pointer itkMaskNoNaN = MaskImageType::New();
  MaskImageType::Pointer itkMorphMask = MaskImageType::New();
  mitk::CastToItkImage(mask, itkMask);
  mitk::CastToItkImage(maskNoNaN, itkMaskNoNaN);
  mitk::CastToItkImage(image, itkFloat);
  mitk::CastToItkImage(morphMask, itkMorphMask);

  int idxA, idxB, idxC;
  switch (direction)
  {
  case 0:
    idxA = 1; idxB = 2; idxC = 0;
    break;
  case 1:
    idxA = 0; idxB = 2; idxC = 1;
    break;
  case 2:
    idxA = 0; idxB = 1; idxC = 2;
    break;
  default:
    idxA = 1; idxB = 2; idxC = 0;
    break;
  }

  auto imageSize = image->GetLargestPossibleRegion().GetSize();
  FloatImageType::IndexType index3D;
  FloatImage2DType::IndexType index2D;
  FloatImage2DType::SpacingType spacing2D;
  spacing2D[0] = itkFloat->GetSpacing()[idxA];
  spacing2D[1] = itkFloat->GetSpacing()[idxB];

  for (unsigned int i = 0; i < imageSize[idxC]; ++i)
  {
    FloatImage2DType::RegionType region;
    FloatImage2DType::IndexType start;
    FloatImage2DType::SizeType size;
    start[0] = 0; start[1] = 0;
    size[0] = imageSize[idxA];
    size[1] = imageSize[idxB];
    region.SetIndex(start);
    region.SetSize(size);

    FloatImage2DType::Pointer image2D = FloatImage2DType::New();
    image2D->SetRegions(region);
    image2D->Allocate();

    MaskImage2DType::Pointer mask2D = MaskImage2DType::New();
    mask2D->SetRegions(region);
    mask2D->Allocate();

    MaskImage2DType::Pointer masnNoNaN2D = MaskImage2DType::New();
    masnNoNaN2D->SetRegions(region);
    masnNoNaN2D->Allocate();

    MaskImage2DType::Pointer morph2D = MaskImage2DType::New();
    morph2D->SetRegions(region);
    morph2D->Allocate();


    unsigned long voxelsInMask = 0;

    for (unsigned int a = 0; a < imageSize[idxA]; ++a)
    {
      for (unsigned int b = 0; b < imageSize[idxB]; ++b)
      {
        index3D[idxA] = a;
        index3D[idxB] = b;
        index3D[idxC] = i;
        index2D[0] = a;
        index2D[1] = b;
        image2D->SetPixel(index2D, itkFloat->GetPixel(index3D));
        mask2D->SetPixel(index2D, itkMask->GetPixel(index3D));
        masnNoNaN2D->SetPixel(index2D, itkMaskNoNaN->GetPixel(index3D));
        morph2D->SetPixel(index2D, itkMorphMask->GetPixel(index3D));
        voxelsInMask += (itkMask->GetPixel(index3D) > 0) ? 1 : 0;

      }
    }

    image2D->SetSpacing(spacing2D);
    mask2D->SetSpacing(spacing2D);
    masnNoNaN2D->SetSpacing(spacing2D);
    morph2D->SetSpacing(spacing2D);

    mitk::Image::Pointer tmpFloatImage = mitk::Image::New();
    tmpFloatImage->InitializeByItk(image2D.GetPointer());
    mitk::GrabItkImageMemory(image2D, tmpFloatImage);

    mitk::Image::Pointer tmpMaskImage = mitk::Image::New();
    tmpMaskImage->InitializeByItk(mask2D.GetPointer());
    mitk::GrabItkImageMemory(mask2D, tmpMaskImage);

    mitk::Image::Pointer tmpMaskNoNaNImage = mitk::Image::New();
    tmpMaskNoNaNImage->InitializeByItk(masnNoNaN2D.GetPointer());
    mitk::GrabItkImageMemory(masnNoNaN2D, tmpMaskNoNaNImage);

    mitk::Image::Pointer tmpMorphMaskImage = mitk::Image::New();
    tmpMorphMaskImage->InitializeByItk(morph2D.GetPointer());
    mitk::GrabItkImageMemory(morph2D, tmpMorphMaskImage);

    if (voxelsInMask > 0)
    {
      imageVector.push_back(tmpFloatImage);
      maskVector.push_back(tmpMaskImage);
      maskNoNaNVector.push_back(tmpMaskNoNaNImage);
      morphMaskVector.push_back(tmpMorphMaskImage);
    }
  }
}